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From Raminder Singh <raminderjsi...@gmail.com>
Subject Re: Phonon task
Date Wed, 30 Jan 2013 17:43:02 GMT
Hi Pedro,

Looks like your machine firewall is blocking the input status socket for gram client. Try
to following the instructions below to solve this. 

1. Create cog.properties in .globus directory (create directory also if not exist)
vi .globus/cog.properties 

tcp.port.range=40000,40100
GLOBUS_TCP_PORT_RANGE=40000,40100

2: update the iptables to allow this port range. Eg -A INPUT  -p tcp --dport 40000:40100 -j
ACCEPT

3. Restart Airavata server and run the job. 

Thanks
Raminder

On Jan 29, 2013, at 4:31 PM, Pedro da Silveira wrote:

> Hi Raminder,
> 
> Thanks for your reply. I am exploring the Airavata Client API. I just
> thought that I should give a try to test my script first using the Xbaya,
> before I tried the workflow on the API.
> 
> Thank you
> 
> 
> 
> 
> On Tue, Jan 29, 2013 at 3:24 PM, Raminder Singh <raminderjsingh@gmail.com>wrote:
> 
>> Gram provider is not able to connect back to your Desktop. Gram client
>> requires global ip for the client machine as well. I face similar problem
>> when i am running jobs from my home. I have to be connected to IU VPN to
>> get the job status otherwise its always zero.
>> 
>> I can help you with getting the outputs. You need to use Airavata API to
>> make it work. This is not integrated in Xbaya. Please look into [1] for API
>> example class to run and monitor the workflow outside XBaya. You can save
>> your workflow in registry and just pass the workflow name to this method to
>> run the workflow. I have other set of sample code here [2].
>> 
>> String setOutputNodeName="<name of the workflow node>"; //CABDone_invoke
>> String setOutputLocation="<local location>";
>> 
>> ExperimentAdvanceOptions options =
>> airavataAPI.getExecutionManager().createExperimentAdvanceOptions(
>>                                workflowName, username, null);
>>                if(experimentName != null && !experimentName.isEmpty()){
>>                options.setCustomExperimentId(experimentName);
>>                }
>> 
>> options.getCustomWorkflowOutputDataSettings().addNewOutputDataSettings(setOutputNodeName,
>> setOutputLocation,
>>                                registryURL, false);
>> String experimentId =
>> airavataAPI.getExecutionManager().runExperiment(workflowName,
>> workflowInputs, options);
>> 
>> 
>> Please let me know if you need more details.
>> 
>> Thanks
>> Raminder
>> 
>> 1.
>> https://svn.apache.org/repos/asf/airavata/trunk/samples/airavata-client/workflow-run/src/main/java/org/apache/airavata/client/samples/RunWorkflow.java
>> 2.
>> https://ogce.svn.sourceforge.net/svnroot/ogce/gateway-staging/odi-astronomy/airavata-api-client/src/main/java/org/apache/airavata/odi/client/WorkflowSubmission.java
>> 
>> On Jan 29, 2013, at 4:03 PM, Pedro da Silveira wrote:
>> 
>>> Hi All,
>>> 
>>> I ran a task on Lonestar using Apache Airavata that took approximately 15
>>> hour to finish. In the end it finishes successfully.
>>> 
>>> I noticed on the log of Apache Airavata that it was constantly printing,
>>> while I was hanging waiting the task to finish. It looks fine, since the
>>> job was taking some time to finish.
>>> 
>>> =============================
>>> [INFO] Status is zero
>>> [INFO] Status is zero
>>> [INFO] Job proxy expired. Trying to renew proxy
>>> org.globus.gsi.gssapi.GlobusGSSCredentialImpl@19d00552
>>> [INFO] Proxy file renewed to
>>> /tmp/x509up_uogce8653d6c7-7eed-4628-abf3-816fb122c8d6 for the user ogce
>>> with 3600 lifetime.
>>> [INFO] Myproxy renewed
>>> [INFO] Status is zero
>>> [INFO] Status is zero
>>> ============================================
>>> 
>>> In the end, my task completed nicely, but at the Xbaya I had this screen:
>>> 
>>> http://i50.tinypic.com/208h08p.jpg
>>> 
>>> <ns:description>The connection to the server failed (check host and port)
>>> [Caused by: Connection refused]:
>>> org.apache.airavata.core.gfac.exception.JobSubmissionFault: The
>> connection
>>> to the server failed (check host and port) [Caused by: Connection
>>> refused]</ns:description>
>>> 
>>> 
>>> At the Airavata-Server log, I had:
>>> 
>>> =================================================================
>>> 
>>> [INFO] Job proxy expired. Trying to renew proxy
>>> org.globus.gsi.gssapi.GlobusGSSCredentialImpl@ef61e4a
>>> [INFO] Proxy file renewed to
>>> /tmp/x509up_uogce6ce97bd7-650c-46fb-8dea-b6f537fecd13 for the user ogce
>>> with 3600 lifetime.
>>> [ERROR] Context passed was NULL.
>>> java.lang.RuntimeException: Context passed was NULL.
>>> at
>>> 
>> org.apache.airavata.workflow.tracking.impl.ProvenanceNotifierImpl.sendingFault(ProvenanceNotifierImpl.java:496)
>>> at
>>> 
>> org.apache.airavata.workflow.tracking.impl.ProvenanceNotifierImpl.sendingFault(ProvenanceNotifierImpl.java:485)
>>> at
>>> 
>> org.apache.airavata.core.gfac.notification.impl.WorkflowTrackingNotification.executionFail(WorkflowTrackingNotification.java:108)
>>> at
>>> 
>> org.apache.airavata.core.gfac.notification.impl.DefaultNotifier.executionFail(DefaultNotifier.java:135)
>>> at
>>> 
>> org.apache.airavata.core.gfac.exception.JobSubmissionFault.sendFaultNotification(JobSubmissionFault.java:52)
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:231)
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.AbstractProvider.execute(AbstractProvider.java:69)
>>> at
>>> 
>> org.apache.airavata.core.gfac.services.impl.AbstractSimpleService.execute(AbstractSimpleService.java:118)
>>> at org.apache.airavata.core.gfac.GfacAPI.gridJobSubmit(GfacAPI.java:140)
>>> at
>>> 
>> org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:256)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:749)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:533)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.scheduleDynamically(WorkflowInterpreter.java:218)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:389)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.access$400(WorkflowInterpretorSkeleton.java:87)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton$2.run(WorkflowInterpretorSkeleton.java:382)
>>> at java.lang.Thread.run(Thread.java:680)
>>> [INFO] -----DATA-----
>>> [INFO] lonestar4.tacc.teragrid.org,&( queue = "normal" )( stdout =
>>> 
>> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/lonestar_application.stdout"
>>> )( count = "64" )( executable =
>>> "/scratch/01437/ogce/Vlab/Phonon/executePhonon.sh" )( stderr =
>>> 
>> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/lonestar_application.stderr"
>>> )( maxwalltime = "1440" )( hostCount = "8" )( minmemory = "10240" )(
>>> project = "TG-STA110014S" )( jobtype = "mpi" )( environment = (
>> "inputData"
>>> 
>> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData"
>>> ) ( "outputData"
>>> 
>> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/outputData"
>>> ) )( proxy_timeout = "1" )( arguments =
>>> 
>> "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Pwscf_Input"
>>> 
>> "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Cd_PON_sp_LDA.vdb"
>>> 
>> "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Te_PON_LDA.vdb"
>>> 
>> "///scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4/inputData/Phonon_Input"
>>> )( directory =
>>> 
>> "/scratch/01437/ogce/Vlab/Phonon//AppZb3_Mon_Jan_28_11_55_05_CST_2013_061ec7d0-33e6-4907-935c-7f8acb87bcd4"
>>> )( maxmemory = "15360" )
>>> [INFO] -----END DATA-----
>>> [ERROR] The connection to the server failed (check host and port) [Caused
>>> by: Connection refused]
>>> org.apache.airavata.core.gfac.exception.JobSubmissionFault: The
>> connection
>>> to the server failed (check host and port) [Caused by: Connection
>> refused]
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:229)
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.AbstractProvider.execute(AbstractProvider.java:69)
>>> at
>>> 
>> org.apache.airavata.core.gfac.services.impl.AbstractSimpleService.execute(AbstractSimpleService.java:118)
>>> at org.apache.airavata.core.gfac.GfacAPI.gridJobSubmit(GfacAPI.java:140)
>>> at
>>> 
>> org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:256)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:749)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:533)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.scheduleDynamically(WorkflowInterpreter.java:218)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:389)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.access$400(WorkflowInterpretorSkeleton.java:87)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton$2.run(WorkflowInterpretorSkeleton.java:382)
>>> at java.lang.Thread.run(Thread.java:680)
>>> Caused by: org.globus.gram.GramException: The connection to the server
>>> failed (check host and port) [Caused by: Connection refused]
>>> at org.globus.gram.Gram.renew(Gram.java:595)
>>> at org.globus.gram.GramJob.renew(GramJob.java:329)
>>> at org.globus.gram.GramJob.renew(GramJob.java:315)
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.utils.JobSubmissionListener.waitFor(JobSubmissionListener.java:72)
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:206)
>>> ... 11 more
>>> Exception in thread "Thread-42"
>>> org.apache.airavata.workflow.model.exceptions.WorkflowRuntimeException:
>>> org.apache.airavata.workflow.model.exceptions.WorkflowException: The
>>> connection to the server failed (check host and port) [Caused by:
>>> Connection refused]
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:392)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.access$400(WorkflowInterpretorSkeleton.java:87)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton$2.run(WorkflowInterpretorSkeleton.java:382)
>>> at java.lang.Thread.run(Thread.java:680)
>>> Caused by:
>> org.apache.airavata.workflow.model.exceptions.WorkflowException:
>>> The connection to the server failed (check host and port) [Caused by:
>>> Connection refused]
>>> at
>>> 
>> org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:321)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.handleWSComponent(WorkflowInterpreter.java:749)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.executeDynamically(WorkflowInterpreter.java:533)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpreter.scheduleDynamically(WorkflowInterpreter.java:218)
>>> at
>>> 
>> org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton.executeWorkflow(WorkflowInterpretorSkeleton.java:389)
>>> ... 3 more
>>> Caused by: org.apache.airavata.core.gfac.exception.JobSubmissionFault:
>> The
>>> connection to the server failed (check host and port) [Caused by:
>>> Connection refused]
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:229)
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.AbstractProvider.execute(AbstractProvider.java:69)
>>> at
>>> 
>> org.apache.airavata.core.gfac.services.impl.AbstractSimpleService.execute(AbstractSimpleService.java:118)
>>> at org.apache.airavata.core.gfac.GfacAPI.gridJobSubmit(GfacAPI.java:140)
>>> at
>>> 
>> org.apache.airavata.xbaya.invoker.EmbeddedGFacInvoker.invoke(EmbeddedGFacInvoker.java:256)
>>> ... 7 more
>>> Caused by: org.globus.gram.GramException: The connection to the server
>>> failed (check host and port) [Caused by: Connection refused]
>>> at org.globus.gram.Gram.renew(Gram.java:595)
>>> at org.globus.gram.GramJob.renew(GramJob.java:329)
>>> at org.globus.gram.GramJob.renew(GramJob.java:315)
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.utils.JobSubmissionListener.waitFor(JobSubmissionListener.java:72)
>>> at
>>> 
>> org.apache.airavata.core.gfac.provider.impl.GramProvider.executeApplication(GramProvider.java:206)
>>> ... 11 more
>>> 
>>> =================================================================
>>> 
>>> My questions:
>>> 
>>> Is there anything that I should do to avoid this error to happen?
>>> What do I have to do transfer one output file "Text File" from Lonestar
>>> back to my Desktop?
>>> 
>>> Thank you,
>>> 
>>> Pedro da Silveira
>> 
>> 


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